Command Line Interface

def convert(args):
    """
    Command-line interface for format conversion operations.

    Provides CLI access to all format conversion functions including
    GFF3, GTF, TBL, GenBank, and protein/transcript extraction with
    flexible filtering and output options.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - input: Input file path
        - fasta: Genome FASTA file path
        - output: Output file path
        - format: Output format (gff3, gtf, tbl, genbank, proteins, etc.)
        - table: Genetic code table
        - grep: Filter patterns to include
        - grepv: Filter patterns to exclude
        - debug: Enable debug output

    Returns:
    None
    """

def consensus(args):
    """
    Command-line interface for EvidenceModeler-like consensus prediction.

    Combines multiple gene prediction sources with protein and transcript
    evidence to generate high-quality consensus gene models using
    configurable weights and validation criteria.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - fasta: Genome FASTA file path
        - genes: List of gene prediction file paths
        - proteins: List of protein alignment file paths
        - transcripts: List of transcript alignment file paths
        - weights: Source weight configuration file
        - output: Output consensus GFF3 file
        - minscore: Minimum score threshold
        - repeats: Repeat annotation file for filtering
        - debug: Enable debug output

    Returns:
    None
    """

def compare(args):
    """
    Command-line interface for annotation comparison analysis.

    Compares two genome annotations to identify differences, calculate
    similarity metrics, and generate detailed comparison reports with
    feature-level analysis and statistics.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - old: Path to reference annotation file
        - new: Path to query annotation file
        - fasta: Genome FASTA file path
        - output: Output comparison report path
        - debug: Enable debug output

    Returns:
    None
    """

def stats(args):
    """
    Command-line interface for annotation statistics calculation.

    Calculates comprehensive statistics for genome annotations including
    gene counts, feature distributions, sequence lengths, and quality
    metrics with detailed reporting options.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - input: Input annotation file path
        - fasta: Genome FASTA file path (optional)
        - output: Output statistics file path
        - format: Output format (text, json, csv)

    Returns:
    None
    """

def sort(args):
    """
    Command-line interface for GFF3 file sorting.

    Sorts GFF3 files by genomic coordinates ensuring proper feature
    ordering and parent-child relationships are maintained.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - input: Input GFF3 file path
        - output: Output sorted GFF3 file path

    Returns:
    None
    """

def sortGFF3(input, output):
    """
    Sort GFF3 file by genomic coordinates.

    Parameters:
    - input (str): Input GFF3 file path
    - output (str): Output sorted GFF3 file path

    Returns:
    None
    """

def sanitize(args):
    """
    Command-line interface for GFF3 file sanitization.

    Cleans and validates GFF3 files by fixing common format issues,
    removing invalid features, and ensuring compliance with GFF3
    specification requirements.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - input: Input GFF3 file path
        - output: Output sanitized GFF3 file path
        - strict: Enable strict validation mode

    Returns:
    None
    """

def rename(args):
    """
    Command-line interface for feature renaming operations.

    Systematically renames annotation features using configurable
    patterns and rules to ensure consistent naming conventions
    across annotation files.

    Parameters:
    - args (argparse.Namespace): Parsed command-line arguments containing:
        - input: Input annotation file path
        - output: Output renamed annotation file path
        - pattern: Renaming pattern specification
        - prefix: Prefix for new feature names

    Returns:
    None
    """

# Convert GFF3 to GTF format
gfftk convert -i annotation.gff3 -f genome.fasta -o output.gtf

# Extract protein sequences
gfftk convert -i annotation.gff3 -f genome.fasta -o proteins.faa --output-format proteins

# Convert with filtering
gfftk convert -i annotation.gff3 -f genome.fasta -o filtered.gff3 --grep product:kinase

# Basic consensus prediction
gfftk consensus -f genome.fasta -g augustus.gff3 genemark.gff3 -p proteins.gff3 -o consensus.gff3

# With custom weights and repeat filtering
gfftk consensus -f genome.fasta -g augustus.gff3 genemark.gff3 \
    -p proteins.gff3 -t transcripts.gff3 \
    -w weights.txt --repeats repeats.bed -o consensus.gff3

# Compare two annotations
gfftk compare --old reference.gff3 --new updated.gff3 -f genome.fasta -o comparison.txt

# Calculate statistics
gfftk stats -i annotation.gff3 -f genome.fasta -o stats.txt

# Sort GFF3 file
gfftk sort -i unsorted.gff3 -o sorted.gff3

# Sanitize GFF3 file
gfftk sanitize -i messy.gff3 -o clean.gff3

# Rename features systematically
gfftk rename -i annotation.gff3 -o renamed.gff3 --prefix GENE

import argparse
from gfftk.convert import convert
from gfftk.consensus import consensus
from gfftk.compare import compare
from gfftk.stats import stats
from gfftk.sort import sort
from gfftk.sanitize import sanitize
from gfftk.rename import rename

# Create argument namespace (equivalent to CLI args)
args = argparse.Namespace(
    input='annotation.gff3',
    fasta='genome.fasta',
    output='output.gtf',
    format='gtf',
    table=1,
    debug=False
)

# Call conversion function
convert(args)